SSU Peaks Positions & ORF

Help & Support
1

Hello,

A quick question regarding positions for peaks. If I run a given variant, expected to cause an intronic cryptic splice site change (both donor and acceptor gain, for instance), and have the following peak data print out for the most relevant peaks in splice-site usage:

ALT SSU(+) peak metadata (±250 bp around variant):
peak_bp height left_height right_height global_bin window_bin bin_size_bp distance_to_center_bp abs_distance_bp
144410630 0.2700 0.0000 0.0002 524288 250 1 1 1
144410738 0.1858 0.0010 0.0011 524397 359 1 109 109

Do the peaks specify the positions of the new canonical donor and acceptor, or the first/last nt of the pseudoexon itself? I.e. what are the positions for the hypothesised ORF?

Thank you

2

Not sure I read your metadata correctly. AG SSU predict usage of splice sites, we define splice sites as first and last base of exons. Therefore the new peaks in ALT SSU are likely corresponding to the first/last base of the cryptic exon. You can also check the splice junction and RNAseq predictions.

3

Thank you that’s really helpful.

So a given exon would be the SSU peaks inclusive (0-based). Ie for the above example with peaks at 144410630 And 144410738, the cryptic exon length is 109 bases?